[R-pkg-devel] vignette error in debian

[Sebastian Meyer]

This is most likely related to the recently changed class of matrices.

R> class(matrix(1))

returned "matrix" but will return c("matrix", "array") in future
versions of R. See the corresponding item in the R-devel NEWS

https://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html

To reproduce the error, you need a fairly recent R-devel and set the
environment variable

_R_CLASS_MATRIX_ARRAY_=true

On CRAN, this configuration is currently only used in the two R-devel
flavors which give warnings for your package.

Happy debugging!

	Sebastian


Am 27.11.19 um 23:16 schrieb Fernando Roa:
> After Ege answer, I could replicate the error(s): list' object cannot be
> coerced to type 'double'
> with CMD check: bash R-devel.sh CMD check --as-cran
> idiogramFISH_1.9.1.tar.gz  in a vmware
> debian guest with the r-devel (4.0) version of R installed after:
> http://singmann.org/installing-r-devel-on-linux/
> 
> Error does not occur in a R-devel console session installed
> in /usr/local/lib/R-devel/bin
> 
> After adding debug prints to the code, problem points to a mapply
> 
> Here are the values I got with debug printing
> 
> labelytoplot<-list(c(0.654545454545455, 0.654545454545455,
> 0.763636363636364, 0.763636363636364), c(0.872727272727273,
> 0.872727272727273, 0.981818181818182, 0.981818181818182),
> c(1.09090909090909, 1.09090909090909, 1.2, 1.2), c(1.30909090909091,
> 1.30909090909091, 1.41818181818182, 1.41818181818182))
> labelxtoplot<-list(c(42.5, 44.75, 44.75, 42.5), c(42.5, 44.75, 44.75,
> 42.5), c(42.5, 44.75, 44.75, 42.5), c(42.5, 44.75, 44.75, 42.5))
> borders<-marks<-c("green","blue","yellow","black")
> 
> CODE producing the error in R CMD check only:
> # plot(1:50)
> mapply(function(x,y,z,w) graphics::polygon(x=x,
>                                            y=y,
>                                            col=z,
>                                            lwd=rep(.5,length(marks) )
>                                            ,border=w
> ),
> x = labelxtoplot,
> y = labelytoplot
> ,z = marks
> ,w = borders
> )
> 
> Grateful for any guidance ,
> 
> 
> 
> 
> 
> 
> On Wed, Nov 27, 2019 at 8:34 AM Ege Rubak <rubak using math.aau.dk> wrote:
> 
>> On 27/11/2019 00.22, Fernando Roa wrote:
>>> - I used a guest debian 10 in vmware in my system, and couldn't replicate
>>> the error installing with R CMD INSTALL ....
>>
>> I guess you should rather run "R CMD check ..." on the tar.gz file to
>> reproduce the error.
>>
>> Hope that helps.
>>
>> /Ege
>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> 
> Original message:
> I got a warning only in debian after submitting package to CRAN.
> I want to replicate the vignette warning of debian in the following link to
> solve it:
> 
> Debian:
> https://win-builder.r-project.org/incoming_pretest/idiogramFISH_1.9.1_20191126_012524/Debian/00check.log
> 1 WARNING
> 
> Warning summary:
> "checking re-building of vignette outputs ... [15s/17s] WARNING
> Error(s) in re-building vignettes:
> 'list' object cannot be coerced to type 'double'" several times
> --
> 
> - I used a guest debian 10 in vmware in my system, and couldn't replicate
> the error installing with R CMD INSTALL ....
> 
> - In R of host, I installed rhub and run
> rhub::check_with_sanitizers() # success
> rhub::check_on_debian() # does not work because of vignette dependencies
> not installed
> rhub::check(platform = "debian-gcc-devel") # does not work because of
> vignette dependencies not installed
> 
> https://pastebin.com/wwhbqcSw
> 
> Grateful for any guidance
> 
>